Computer Lab
From phys824
Jump to navigationJump to search
Installing Python and course related packages
- Install Anaconda
- Install KWANT package:
conda install -c conda-forge kwant
- Install PythTB package:
pip install pythtb --upgrade
- Install and test ASE package:
pip install --upgrade --user ase python -m ase test
- GPAW package can be easily installed using Anaconda on Linux or MacOS
- If you want to add RISE package for Jupyter notebooks, execute:
conda install -c conda-forge rise
JUPYTER notebooks for hands-on practice
- Getting started with Python
- Getting started with NumPy and SciPy
- Getting started with Matplotlib
- Nanostructures in equilibrium with Python
- Nanostructures in equilibrium with PythTB
- Nanostructures out of equilibrium with Python
- Nanostructures in equilibrium with KWANT
- Nanostructures out of equilibrium with KWANT
- Superconducting nanostructures with KWANT
JUPYTER notebooks tips and tricks
- Force Jupyter notebook to display all outputs of a give cell (and not just the last one as default):
from IPython.core.interactiveshell import InteractiveShell InteractiveShell.ast_node_interactivity = "all"
- How do you know that Jupyter notebook is running:
- Cell Number Indicator: When a cell is actively executing, the input prompt on the left side of the cell will display an asterisk In [*] instead of a number. Once the execution is complete, the asterisk will be replaced by a sequential number In [1], In [2], etc.
- Kernel Status Indicator: In the top-right corner of the Jupyter Notebook interface, there is a small circle. This circle indicates the kernel's status:
- Solid/Grey: The kernel is busy, meaning a cell is currently executing.
- Empty/White: The kernel is idle, meaning no cells are currently executing.
- Executing this command will display a list of all running Jupyter Notebook servers, including their URLs and the ports they are using.
jupyter notebook list
Python references
- J. M. Stewart and M. Mommert, Python for Scientists (Cambridge University Press, Cambridge, 2023). [PDF] + Jupyter notebooks for each Chapter
- Scipy lecture notes
- NumPy: Absolute Beginners Tutorial
- NumPy: Quickstart tutorial
- NumPy for Matlab users
- Timing Python script performance:
def fibonacci(n):
"""Calculate the n-th Fibonacci number using recursion."""
if n <= 0:
return 0
elif n == 1:
return 1
else:
return fibonacci(n - 1) + fibonacci(n - 2)
import time
start = time.perf_counter()
result = fibonacci(40)
end = time.perf_counter()
elapsed = end - start
print(f'Time taken: {elapsed:.6f} seconds')
KWANT references
- KWANT documentation
- VIDEO: Introduction to KWANT
- Learning KWANT through examples
- Selecting matrix solvers in KWANT
- KWANT tools
Density functional theory with GPAW package
How to run GPAW on ulam
GPAW has been installed on ulam with the OS installed python 2.6.
- in order to use the serial version of GPAW type:
python your_gpaw_program.py
- in order to use the parallel version of gpaw use the following syntax (replace 8 with the number of cores you want to use):
mpirun -np 8 gpaw-python_openmpi your_gpaw_program.py
Getting started with GPAW
- VIDEO Tutorial: Electronic structure calculations with GPAW
- VIDEO Tutorial: Short overview of GPAW
- VIDEO Longer overview of GPAW
- VIDEO Tutorial: CO molecule
- Plotting CO wavefunction
- relax.py used in VIDEO Tutorial:
from ase import Atoms
from ase.io import write
from ase.optimize import QuasiNewton
from gpaw import GPAW
d = 1.10 # Starting guess for the bond length
atoms = Atoms('CO', positions=((0, 0, 0),
(0, 0, d)), pbc=False)
atoms.center(vacuum=4.0)
write('CO.cif', atoms)
calc = GPAW(h=0.20, xc='PBE', txt='CO_relax.txt')
atoms.set_calculator(calc)
relax = QuasiNewton(atoms, trajectory='CO.traj', logfile='qn.log')
relax.run(fmax=0.05)
- ASE tutorials
- Basics of GPAW calculations
- Band structure of Ni plotted in three steps
- Lattice constant, DOS, and band structure of Si
- STM simulations
GPAW Exercises Related to Midterm Project
- Band structure of bulk graphene
- Subband structure of graphene nanoribbons
- Subband structure of carbon nanotubes
References
- Electronic structure calculations with GPAW: a real-space implementation of the projector augmented-wave method, J. Phys.: Condens. Matter 22, 253202 (2010). [PDF]
- Parameters selection in GPAW scripts
- LCAO basis set in GPAW
- Parameters selection in ASE to define atomic coordinates
- Density of States in GPAW
- About k-point sampling
First-principles quantum transport calculations using NEGF+DFT within GPAW package
Theory Background
- Crash course on NEGF+DFT codes
- NEGF+DFT within GPAW - see also J. Chen, K. S. Thygesen, and K. W. Jacobsen, Ab initio nonequilibrium quantum transport and forces with the real-space projector augmented wave method, Phys. Rev. B 85, 155140 (2012). [PDF]
- M. Strange, I. S. Kristensen, K. S. Thygesen, and K. W. Jacobsen, Benchmark density functional theory calculations for nanoscale conductance, J. Chem. Phys. 128, 114714 (2008). [PDF]
- D. A. Areshkin and B. K. Nikolić, Electron density and transport in top-gated graphene nanoribbon devices: First-principles Green function algorithms for systems containing a large number of atoms, Phys. Rev. B 81, 155450 (2010). [PDF]
